A natural uORF variant confers phosphorus acquisition diversity in soybean

Phosphorus (P) is an essential element for all organisms. Because P fertilizers are a non-renewable resource and high fixation in soils, sustainable agriculture requires researchers to improve crop P acquisition efficiency. Here, we report a strong association signal at a locus of CPU1 (component of phosphorus uptake 1), from a genome-wide association study of P acquisition efficiency in a soybean core collection grown in the field. A SEC12-like gene, GmPHF1, is identified as the causal gene for CPU1. GmPHF1 facilitates the ER (endoplasmic reticulum) exit of the phosphate transporter, GmPT4, to the plasma membrane of root epidermal cells. A common SNP in an upstream open reading frame (uORF) of GmPHF1, which alters the abundance of GmPHF1 in a tissue-specific manner, contributes to P acquisition diversity in soybean. A natural genetic variation conditions diversity in soybean P acquisition, which can be used to develop P-efficient soybean genotypes.

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The Illumina sequencing data generated in this study have been deposited in NCBI (National Center for Biotechnology Information) under SRA (Sequence Read Archive) accession number SRR11929594-SRR11929867 of PRJNA633739 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA633739). In the study, Phytozome database (https://phytozome.jgi.doe.gov/) was used to retrieve the gene's expression levels and annotations; Soybean Expression Atlas database (https:// venanciogroup.uenf.br/cgi-bin/gmax_atlas/index.cgi) was used to retrieve genes' expression levels of multiple tissues. All data is available in the manuscript or the supplementary materials. Source data are provided with this paper.
For genetic mapping, sample size is determined based on i) the requirement of mapping power (referring to a published paper titled "Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice" (doi: 10.1038/ng.3596), which efficiently identified GWAS loci using only 176 samples/accessions) and ii) the workload of field phenotyping (a randomized complete block design with four biologically independent replications). As a result, we indeed detected a genetic locus with a strong signal, CPU1, of which the causal gene was identified and validated in our study. For molecular and physiological experiments, at least three biologically independent samples were used to derive statistics.
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Seedlings were grown randomly in the growth chamber. For the field experiment, a randomized complete block design was followed.
The experiments were not blinded, but repeated by multiple independent experiments to reduce bias. A randomized complete block design with four biologically independent replications was adopted in field phenotyping. As a result, a credible genetic locus was identified and the causal gene was identified and validated in our study. Data analyses were blinded to plant selection.
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